Our team constructed a cross-sectional atlas using six modalities, including LFB (Luxol Fast Blue) staining of tissue slices, pseudo-colored LFB staining, sectional specimen images, high-resolution MRI, dMRI sectional tractography and fiber orientation distribution (constrained spherical deconvolution-CSD) maps. The atlas was created from the same monkey brain’s ex-vivo MRI and histology dataset with an interval of 800μm per slice. The website-based display of this atlas is divided into two main types. The first type is an interactive interface with anatomical name tags. We marked the main anatomical names in the first four modalities, and clicking on the corresponding anatomical names displays the corresponding location in the atlas. It also allows comparison with the directional information of the two dMRI modalities. The second type is superimposed-scaling display, which superimposes other different modalities on the “Histo: luxol fast blue (LFB)”and allow adjustment of transparency to distinguish the interested anatomical structure better. It can also be zoomed in for observation, which is mainly for the “Histo: luxol fast blue (LFB)” and “Histo: Primary fiber orientation (HSB)” (with the other modalities are interpolated and scaled accordingly), with a maximum magnification to a single pixel size of 0.886*0.886μm2 for a more detailed understanding of the subtle structure.
●Histo: luxol fast blue (LFB)
LFB stained histology to visualize myelinated structures (nerve fibers) in the brain. Here the original image (resolution ≈ 0.443 microns/pixel) has been downsampled to around 0.886 micron/pixel resolution.
●Histo: Primary fiber orientation (HSB)
Images were digitally color-coded based on the local orientation in the pixelwise (0.886*0.886μm2) STA (Structure Tensor Analysis), which allowed direct visualization of white matter complexity at the microscopic level.
●Sectional specimen: Blockface images
The most traditional modality is direct observation of the specimen by naked eye, which gives a relatively intuitive understanding of gray and white matter structures.
●MRI: Structural
High resolution Structural MRI (GRE) revealing grey & white matter contrast with detailed level in the brain.
●MRI: Sectional tractography
Achieved through DSI studio, the diffusion data were reconstructed using generalized q-sampling imaging, and a deterministic fiber tracking algorithm was used. This modality shows the orientation and spatial relationships of fiber bundles.
●MRI: Fiber orientation distribution (from CSD)
Obtain the FOD (Fiber orientation distribution) using MRtrix3 by CSD fitting. Through the FOD within each voxel, one can easily distinguish the heterogeneity and orientation (cross-fiber direction) of the nerve fibers.
